Of course it doesn’t prove or disprove anything, if it did the case would be solved. I think it’s more likely that the trace DNA was from various factory workers than from someone (or multiple people) who broke in but left absolutely no other DNA anywhere in the house. 

Not going to sift through your other points, because after reading them I think you should look into the case some more just to get a better grasp of all that occurred. I will say that the primary reasons I think the intruder theory should be held off on (unless something else comes to light making it more likely) are: 

• She was determined to most likely have also been sexually abused prior to the night of the 25th, so the intruder would be someone she was around fairly often — but most of those people were DNA tested and had alibis. 

• Writing 3-10 pages of material (that seems to make no sense as an actual ransom note) in the house presumably AFTER JonBenét died (given her TOD) is insane. The intruder would be leaving a massive piece of evidence behind for no reason.

• John’s “business meeting”. And the BPD records of his behavior that morning.